<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">Thanks a lot Justin. It worked really nice. <br><br>now I am stuck with another problem. I need to add the Building block GTP and GDP in 43a1, as I need to get the topology of a tubulin monomer. I got the file from a old post here. <br><br><span><a target="_blank" href="http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html">http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html</a></span><br><br>I copied and pasted it into my file, yet, as the structure doesn't match it gave several errors. <br><br>is there any way to fix this?<br><br>Thanks a lot for your help. <br><br>Tawhid<br><br><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original
Message ----<br>From: Justin A. Lemkul <jalemkul@vt.edu><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Monday, November 26, 2007 7:14:43 PM<br>Subject: Re: [gmx-users] pdb2gmx error<br><br>
Quoting Tawhid Ezaz <<a ymailto="mailto:ezaztaw@yahoo.com" href="mailto:ezaztaw@yahoo.com">ezaztaw@yahoo.com</a>>:<br><br>> Hi,<br>><br>> I have just started to learn gromacs. I am facing a problem to make
topology<br>> file of a myoglobin. I got the pdb file from the csc tutorial.<br>><br>> When i am running the pdb2gmx with<br>><br>> pdb2gmx -f conf.pdb -p topol.top<br>><br>> i get the message, HEME148 CAB1428 0.569<br>> HEME148 CAC1437 0.562 0.820<br>> N-terminus: NH3+<br>> C-terminus: COO-<br>> Now there are 148 residues with 1451 atoms<br>> -------------------------------------------------------<br>> Program pdb2gmx, VERSION 3.3.1<br>> Source code file: pdb2top.c, line: 570<br>><br>> Fatal error:<br>> atom N not found in residue 1ACE while combining tdb and rtp<br>> -------------------------------------------------------<br>><br>> I was using 43a1 force field (0), {but none of them works}.<br>><br>> i read some previous post and got the idea that there should be a N
atom with<br>> should be linked with ACE, but my conf.pdb files does not have any. I
have<br>> topol.top file from the tutorial but didn't show how I can generate
that.<br><br>Use the -ter option with pdb2gmx, and select 'none' when prompted.
That way,<br>pdb2gmx does not look for an N-terminal nitrogen (which is obviously
absent in<br>an acetyl group).<br><br>-Justin<br><br>><br>> I am a totally newbie, thus I am wondering what should I do. Which
file I<br>> should correct to get rid of those? Do I need to know the bonding of
every<br>> atom in the molecule for that?<br>><br>> Thanks in advance<br>><br>> Tawhid<br>><br>><br>><br>><br>><br><br><br><br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br><br>========================================<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search
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